Thursday, March 22, 2007

Integrative Bioinformatics

Integrative Bioinformatics (IB) has emerged as the label of choice to describe the development of integrated data management and data analysis infrastructure for the life sciences. The elaboration of the technology required, the sophistication of computational statistics methodologies involved, and the potential for formal abstract representation of very complex Biological phenomena systemically, has led to the coalescence of Integrative Bioinformatics as a research topic of its own. Accordingly, a graduate research program was put in place to train newcomers in this field.

The graduate training in integrative bioinformatics includes a formal program covering founding elements of Biology, Computer Science and Statistics. However, the defining characteristic of the training program, and indeed of the research practice is this field, is its integrative focus. Accordingly, this material is delivered in a problem solving format geared towards the identification and deployment of algorithmic solutions that interoperate with the global, mostly public, suite of bioinformatic resources. This choice of format also anticipates the graduate research itself which includes bioinformatic tool making.

Active courses:

Integrative Bioinformatics 2008 [GS01 0123]

Location HMB 13.356, Tuesdays and Thursdays 11am-1pm


  1. [Jan 8] - Introduction (Jonas)
  2. [Jan 15] - Introduction to programming and data structures in MATLAB. (Jonas)
  3. [Jan 17] - Algorithm deployment illustrated for alignment as a metric. (Jonas)
  4. [Jan 22] - Data structures and data services (Pablo, Jonas)
  5. [Jan 24] - hands on session developing a client for UCSC Genome Browser (everybody)
  6. [Jan 29] - Document object model (DOM) and XML as vehicles for interoperability.
  7. [Jan 31] - Dynamic programming and regular expression homework.
  8. [Feb 05] - Design and practice of Graphic User Interface development.
  9. [Feb 07] - more on GUIs. Discussion of the DILS 2008 challenge.
  10. [Feb 12] - S3DB: a distributed, semantically explicit, RESTful, DBMS.
  11. [Feb 14] - Continuation of last class: S3DB.
  12. [Feb 19] - Homework review of UCSC client (Diogo > Lena > Chunyan > Rys > David)
  13. [Feb 21] - Common Standards vs Common Protocols [Romesh Stanislaus presents]
  14. [Feb 26] - GUI example 1/4 : TCGA client.

Past courses:

Integrative Bioinformatics 2007

Location HMB 13.356, Thursdays 2-4 pm

  1. [March 29 ] - Introduction (Jonas)
  2. [April 5] - Introduction to Data Structures (Jonas)
  3. [April 12] - Semantic constructs using S3DB (Lena)
  4. [April 19] - XML constructs (Romesh & Lena)
  5. [April 27] - Case Study: Ovary Cancer data integration at the Kleberg Foundation (Jonas)
  6. [May 3] - Menial Bioinformatics - modelling strings for parsing data files (Jonas).
  7. [May 10] - XSLT, XPath, XQuery, XML I/O.
  8. [May 16] - NO CLASS TODAY, we are participating in SOA meeting at MDACC. If you want to attend please email me (Jonas) and I'll send you the directions to teh seminar room.
  9. [May 24] - Last session: overview of multivariate exploratory and disciminant statistical analysis methods. Here's the good bey and thank you Note, in 2008 we hope to have IB as a formal topic of GSBS:

-------- Original Message --------
Subject: Classes are over
Date: Thu, 31 May 2007 09:59:02 -0500
From: Jonas S Almeida
To: Helena Deus , Jonas Almeida ,,,, Helena Deus ,,,, Pablo Freire , Katherine Hale

Hi everybody,just in case any of you missed this and is heading for the integrative bioinformatics class today: the classes ended last week with the overview of multivariate exploratory and discriminant analysis methods. I also want to take this opportunity to thank you all so much for your participation in this class. A special thank you to Katherine for bringing her datasets and Biology problems to the table and sharing them with us. I look forward to keep interacting with you. Maybe we should set specialized workshops to frame specific collaborations. In any case, I'll use this first run of the Integrative Bioinformatics class to request it to be added as a subject of GSBS.cheers,

JonasJonas S Almeida, Professor
Dept Bioinformatics and Computational Biology
Univ. Texas MDAnderson Cancer Center - unit 237
1515 Holcombe Blvd, Houston TX 77030-4009, USA
Tel: 713 792 9875 ;
fax: 305 574 5818

1 comment:

Gábor said...

Great to hear this class is starting.

I would be interested in teaching one or more sessions on modeling the dynamics of gene regulatory and signaling networks. I could cover various modeling methods (Boolean, continuous ODE, stochastic).

The aim would be to create an interface between experimentalists and theoreticians working on the dynamics of small networks.

I would like to find out if there is interest in such a topic.